4DG6

Crystal structure of domains 1 and 2 of LRP6

PDB DOI: https://doi.org/10.2210/pdb4DG6/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2012-01-25 Released: 2012-06-13
Deposition Author(s): Ceska, T.A., Doyle, C., Slocombe, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.313
R-Value Work: 0.257
R-Value Observed: 0.257

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Characterization of the interaction of sclerostin with the LRP family of Wnt co-receptors

Holdsworth, G., Slocombe, P., Doyle, C., Sweeney, B., Veverka, V., Le Rich, K., Franklin, R.J., Brookings, D., Turner, J., Kennedy, J., Garlish, R., Shi, J., Newnham, L., McMillan, D., Muzylak, M., Carr, M., Henry, A.J., Ceska, T., Robinson, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 71.07 kDa
Atom Count: 5,005
Modelled Residue Count: 616
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	A	616	Homo sapiens	Mutation(s): 0 Gene Names: LRP6
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens) Explore O75581 Go to UniProtKB: O75581
PHAROS: O75581 GTEx: ENSG00000070018
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75581
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation	Interactions Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain B Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.313
R-Value Work: 0.257
R-Value Observed: 0.257
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.36	α = 90
b = 109.36	β = 90
c = 130.88	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Ceska, T.A.

Doyle, C.

Slocombe, P.

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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Deposit Data

Help and Resources

4DG6

Crystal structure of domains 1 and 2 of LRP6

Characterization of the interaction of sclerostin with the LRP family of Wnt co-receptors

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)